Date: 2018-08-17
R version: 3.5.0
Corresponding author: matthew.malishev@gmail.com
This document can be found at https://github.com/darwinanddavis/SchistoMesocosm
Follow instructions in code chunks labelled ‘fileoutput’ to toggle pdf of plots saved to directory on/off (‘Size_per_tank_over_time.pdf’)
This document uses the schisto mesocosm 2016 data to explore cercariae production from snail hosts of different body sizes (diameter in mm and mass in mg) over a 14 week period under high and low N/P nutrient conditions. Host reproduction (egg masses) is also calculated.
wd <- params$dir # working dir is set in yaml header
setwd(paste0(wd,"/"))
f <- "meso1_.csv"
f2 <- "meso2_.csv" 'data.frame': 720 obs. of 13 variables:
$ Tank : int 1 2 3 4 5 6 7 8 9 10 ...
$ NP : chr "High" "Low" "Low" "High" ...
$ Size : chr "Small" "Intermediate" "Intermediate" "Small" ...
$ Schisto : chr "No" "Yes" "Yes" "Yes" ...
$ Week : int 0 0 0 0 0 0 0 0 0 0 ...
$ Snail : int 60 60 60 60 60 60 60 60 60 60 ...
$ Total_Biomass : num 96 620.6 670.5 86.7 121.4 ...
$ Cercarial_production: int 0 0 0 0 0 0 0 0 0 0 ...
$ Infected_abundance : int 0 0 0 0 0 0 0 0 0 0 ...
$ Sampling_Effort : int NA NA NA NA NA NA NA NA NA NA ...
$ Eggs : int NA NA NA NA NA NA NA NA NA NA ...
$ Phyto_F : num NA NA NA NA NA NA NA NA NA NA ...
$ Peri_F : num NA NA NA NA NA NA NA NA NA NA ...
Set plotting parameters
Get only infected snails
Mesocosm 1 data sheet
Shell diameter (mm) per tank
Welch Two Sample t-test
data: Diameter and Tank
t = -292.67, df = 54609, p-value < 2.2e-16
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-19.45879 -19.19989
sample estimates:
mean of x mean of y
5.821956 25.151292
xchar= 0.7875 ; (yextra,ychar)= -0.004785 0.004785
points2( 30.85 30.85 , 0.1 0.09522 , pch= 20 20 , ...)
Shell diameter (mm) over time (weeks)
~1000 eggs inoculated at 0,2,4,6 weeks
For all tanks (n = 48), see ‘Size_per_tank_over_time.pdf’ in /Users/malishev/Documents/Emory/research/mesocosm
~1000 eggs inoculated at 0,2,4,6 weeks
Select tank. Max 48
tank <- 12 # Select tank #. Max 48
paste0("Tank ",tank) [1] "Tank 12"
See “Size_per_tank_over_time_HIGH.pdf” in /Users/malishev/Documents/Emory/research/mesocosm
See “Size_per_tank_over_time_LOW.pdf” in /Users/malishev/Documents/Emory/research/mesocosm
See “Size_per_tank_over_time_HIGH_LARGE.pdf” in /Users/malishev/Documents/Emory/research/mesocosm
See “Size_per_tank_over_time_LOW_LARGE.pdf” in /Users/malishev/Documents/Emory/research/mesocosm
See “Size_per_tank_over_time_HIGH_SMALL.pdf” in /Users/malishev/Documents/Emory/research/mesocosm
See “Size_per_tank_over_time_LOW_SMALL.pdf” in /Users/malishev/Documents/Emory/research/mesocosm
(Soft tissue dry mass in mg = 0.0096 * Diameter[in mm]^3)
~1000 eggs inoculated at 0,2,4,6 weeks
Biomass Cercariae
6469 244.7544 0
Without max value of as.numeric(outer)[1]
Point size by cercariae number
Linear log
Shell diameter (mm)
Select tank. Max 48
[1] "Tank 24"
Cercariae shed over 90 mins per week
~1000 eggs inoculated at 0,2,4,6 weeks
Snail abundance over time (weeks)
Select tank. Max 48
[1] "Tank 24"
[1] 2300
Mesocosm 2 data sheet
phyto = flourescence units
peri = flourescence per 2 weeks / 3.5 inch^2 tile (gross productivity biomass rate)
~1000 eggs inoculated at 0,2,4,6 weeks
xchar= 3.937 ; (yextra,ychar)= -0.001435 0.001435
points2( 147.7 147.7 147.7 , 0.03072 0.02928 0.02785 , pch= 20 20 20 , ...)
~1000 eggs inoculated at 0,2,4,6 weeks